Nextflow Registry | nf-core/varscan/processsomatic@0.0.0-6c4ed3a

nf-core/varscan/processsomatic @ 0.0.0-6c4ed3a

VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. This subtool divides variants based on status (germline, somatic, loss of heterozygosity) and confidence level (high-confidence or not) and outputs them in separate VCF files.

variant calling germline somatic vcf variants genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 2

Source: nf-core/modules

Authors: @vmelichar

Maintainers: @vmelichar

Summary

Get started

Add the following snippet to your workflow script to include this module.

include { VARSCAN_PROCESSSOMATIC } from 'nf-core/varscan/processsomatic'

License

MIT License

Process

`Name`	`VARSCAN_PROCESSSOMATIC`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	VCF file `*.{snvs,indels}.vcf.gz`

Output 7 channels

#1 loh_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.LOH.vcf.gz` file	VCF file with loss of heterozygosity variants `*.LOH.vcf.gz`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 loh_hc_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.LOH.hc.vcf.gz` file	VCF file with high-confidence loss of heterozygosity variants `*.LOH.hc.vcf.gz`

#4 somatic_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Somatic.vcf.gz` file	VCF file with somatic variants `*.Somatic.vcf.gz`

#5 germline_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Germline.vcf.gz` file	VCF file with germline variants `*.Germline.vcf.gz`

#6 somatic_hc_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Somatic.hc.vcf.gz` file	VCF file with high-confidence somatic variants `*.Somatic.hc.vcf.gz`

#7 germline_hc_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.Germline.hc.vcf.gz` file	VCF file with high-confidence germline variants `*.Germline.hc.vcf.gz`

Tool	Description	Homepage
varscan	variant detection in massively parallel sequencing data	https://github.com/dkoboldt/varscan

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:51:52 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fvarscan%2Fprocesssomatic/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/varscan/processsomatic/blobs/sha256:e67ff6d598c6d15b4a898df1f38fa37d4c709d4efec5728ada70f1d3a4e20343
Size	3.2 KB
Checksum	sha256:e67ff6d598c6d15b4a898df1f38fa37d4c709d4efec5728ada70f1d3a4e20343
Downloads	1

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a